The original gapped BLAST with statistics, providing the performance, features and reliability demanded by technical professionals:

• AB-BLAST ... setting a higher standard

The latest release is dated [17-Mar-2020] and is free for personal, nonprofit use.
Licensing and download information is available <here>.

If you're not using AB-BLAST, you don't know what you're missing!

Announcements

[07-Feb-2007] Troubled by the letters “J”, “O” or “U” in amino acid sequences?   Read this.
[24-Aug-2006] fast 64-bit binaries are now available for Apple “Core 2” systems, including the 8-core Mac Pro
[18-Mar-2006] If system panics occur with 64-bit binaries under Mac OS X 10.4, restrict searches to one CPU (cpus=1)
[09-Jun-2005] “Universal” binaries are now available for Mac OS X 10.4 on Intel and PowerPC processors
[21-May-2005] 64-bit Solaris™ X64 is now supported
[22-Mar-2005] Tabular and XML output are now supported; See the mformat option.
[10-Dec-2003] Licensing of BLAST 2.0 for academic and nonprofit use can now be performed on-line.

Documentation and manuscripts viewable with Acrobat Reader

• AB-BLAST Command Line Options (in PDF here)
• AB-BLAST Parameters Diagram
• Want to see BLAST fly? (updated 27-Apr-2004)
• FAQ: Indexing of Sequence Identifiers with the AB-BLAST Package
• (Old) BLAST Manual, while originally written for NCBI- and WU-BLAST version 1.4, it maintains relevance to AB-BLAST but doesn't cover gapped alignments or the many newer options.

• Basic Local Alignment Search Tool, text of the original BLAST paper
• Introduction to Alignment Scoring Statistics
• Identification of Protein Coding Regions by Database Similarity Search, the original BLASTX manuscript.
• Improved Sensitivity of Nucleic Acid Database Searches Using Application-Specific Scoring Matrices
• Combined Use of Sequence Similarity and Codon Bias for Coding Region Identification

Software that layers on top of BLAST

• BPlite:  a PERL module for parsing BLAST output (I. Korf)
• RepeatMasker (A. Smit et al.) accelerate masking 30-fold or more (Bedell et al., 2000)
• MPBLAST:  multiplex BLASTN queries for a 10-fold speed improvement; and other fancy PERL scripts (Korf and Gish, 2000)
• Sample WWW BLAST Scripts
• Experimental BLAST network service client & server
• XBLAST:  mask query sequences of similar segments reported in BLAST output, to facilitate further downstream processing (J-M Claverie)

BLAST support programs

• Nonredundant database software (version 2) updated [1999-Nov-11]
• SEG filter (Wootton & Federhen) updated [1999-Oct-08]
• XNU filter (Claverie & States)
• DUST filter (Tatusov & Lipman) updated [2000-Jun-05]

Miscellaneous

• BLAST Database Format Descriptions

Archived, public domain source code of old versions of BLAST

• WU-BLAST version 1.4 sequence database search programs
• Precompiled WU-BLAST version 1.4 executables for UNIX
• Old BLAST version 1.3 database search programs, including "BLASTC"
• Crusty, old BLAST version 1.1 database search programs
• DFA (deterministic finite-state automaton) library used in early versions of BLAST

Acknowledgements

AB-BLAST is a product of Advanced Biocomputing, LLC, and is derivative of WU-BLAST 2.0.

Development and support of WU-BLAST 2.0 and AB-BLAST has been made possible in part over many years by equipment loans, gifts or grants from Advanced Micro Devices, Apple, Dell, Hewlett-Packard, IBM, Intel and Sun Microsystems, all of whose generous support has been greatly appreciated.

Please address questions, suggestions and problem reports to: 

Copyright © 2008 Advanced Biocomputing, LLC. All Rights Reserved.